Variant report

Variant	rs8027661
Chromosome Location	chr15:82473593-82473594
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:82472620..82475056-chr15:82476421..82478115,2	MCF-7	breast:
2	chr15:82471168..82473775-chr15:82477385..82479321,2	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11073036	0.93[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs11630197	0.91[ASW][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs11631813	0.81[ASW][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs11639440	0.94[JPT][hapmap]
rs11854289	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11854483	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12324875	0.90[ASW][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs1501367	0.81[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs1566559	0.81[ASN][1000 genomes]
rs1566560	0.81[ASN][1000 genomes]
rs1566561	0.95[ASN][1000 genomes]
rs16973457	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1846908	0.81[ASN][1000 genomes]
rs1948741	0.92[ASN][1000 genomes]
rs1948742	0.85[CHB][hapmap];0.91[ASN][1000 genomes]
rs1972460	0.93[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs2016372	0.96[ASN][1000 genomes]
rs2047679	0.81[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs2134046	0.91[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs2457497	1.00[ASW][hapmap];0.90[CEU][hapmap];0.85[CHB][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2665103	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs28522807	0.82[ASN][1000 genomes]
rs3759800	0.81[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs3858953	0.85[ASN][1000 genomes]
rs3902959	0.81[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs4238534	0.91[ASW][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs4267268	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4296215	0.93[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs4778674	0.80[ASN][1000 genomes]
rs4778986	0.92[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs4778987	0.90[ASW][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs4778990	0.80[ASN][1000 genomes]
rs56398167	0.90[ASN][1000 genomes]
rs61554133	0.93[ASN][1000 genomes]
rs7167504	0.91[ASN][1000 genomes]
rs7176926	0.81[ASN][1000 genomes]
rs72749540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72749543	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72749557	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72749560	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72749561	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72749564	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72749575	0.90[ASN][1000 genomes]
rs72749586	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7403041	0.80[ASN][1000 genomes]
rs7403244	0.81[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs8025964	0.90[ASN][1000 genomes]
rs8027301	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8030210	0.92[ASN][1000 genomes]
rs8030250	0.93[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs8032633	0.92[ASN][1000 genomes]
rs8033313	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs905450	1.00[ASW][hapmap];0.95[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9972440	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv457212	chr15:82454283-82573255	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv570243	chr15:82454283-82573255	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv457213	chr15:82456227-82573255	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv570244	chr15:82456227-82573255	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv570245	chr15:82456227-82591082	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1041040	chr15:82465124-82606410	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv1801737	chr15:82468455-82589044	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs8027661	LOC402057	trans	multi-tissue	Pritchard
rs8027661	LOC653344	cis	multi-tissue	Pritchard
rs8027661	RASGRF1	cis	cerebellum	SCAN
rs8027661	FAM154B	cis	cerebellum	SCAN
rs8027661	BTBD1	cis	cerebellum	SCAN
rs8027661	FAM154B	cis	parietal	SCAN
rs8027661	RP11-152F13.8	cis	Esophagus Mucosa	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:82432600-82476400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr15:82432600-82552800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr15:82444600-82495800	Weak transcription	Fetal Intestine Small	intestine
4	chr15:82455400-82475200	Weak transcription	Brain Hippocampus Middle	brain
5	chr15:82455400-82475200	Weak transcription	Pancreas	Pancrea
6	chr15:82455600-82475200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr15:82456000-82475800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr15:82456000-82475800	Weak transcription	Lung	lung
9	chr15:82456000-82510000	Weak transcription	Thymus	Thymus
10	chr15:82456200-82475200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr15:82456200-82475600	Weak transcription	Fetal Brain Female	brain
12	chr15:82456400-82474200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr15:82456400-82475200	Weak transcription	Fetal Muscle Leg	muscle
14	chr15:82456400-82475200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr15:82456400-82475400	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr15:82456400-82475800	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr15:82456400-82480600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr15:82456400-82487000	Weak transcription	Primary B cells from peripheral blood	blood
19	chr15:82456400-82502200	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr15:82456400-82502400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr15:82456400-82502600	Weak transcription	Duodenum Mucosa	Duodenum
22	chr15:82456400-82502800	Weak transcription	Gastric	stomach
23	chr15:82456400-82505400	Weak transcription	Dnd41	blood
24	chr15:82456400-82505600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr15:82456400-82505600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr15:82456600-82474200	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr15:82456600-82474400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr15:82456600-82474400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr15:82456600-82478600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr15:82456600-82497400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr15:82456800-82475200	Weak transcription	Liver	Liver
32	chr15:82456800-82509800	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr15:82458200-82504800	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr15:82458600-82475600	Weak transcription	GM12878-XiMat	blood
35	chr15:82458600-82479200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr15:82458800-82502800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:82460800-82474000	Weak transcription	Adipose Nuclei	Adipose
38	chr15:82460800-82475200	Weak transcription	Primary T cells from cord blood	blood
39	chr15:82462000-82475800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr15:82462000-82505800	Weak transcription	Primary B cells from cord blood	blood
41	chr15:82464000-82475400	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr15:82464000-82494800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr15:82464200-82476600	Weak transcription	Hela-S3	cervix
44	chr15:82465000-82510000	Weak transcription	Placenta	Placenta
45	chr15:82467200-82473800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr15:82467400-82475200	Weak transcription	Brain Substantia Nigra	brain
47	chr15:82469000-82474000	Enhancers	Osteobl	bone
48	chr15:82469600-82475200	Weak transcription	Brain Anterior Caudate	brain
49	chr15:82470000-82474000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr15:82470200-82474200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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